from __future__ import division, print_function, absolute_import import sys import os import gc import re import threading from nose import SkipTest import numpy as np from numpy.testing import (assert_raises, assert_equal, dec, run_module_suite, assert_, assert_allclose) from scipy.sparse import (_sparsetools, coo_matrix, csr_matrix, csc_matrix, bsr_matrix, dia_matrix) from scipy.sparse.sputils import supported_dtypes from scipy._lib._testutils import xslow def test_exception(): assert_raises(MemoryError, _sparsetools.test_throw_error) def test_threads(): # Smoke test for parallel threaded execution; doesn't actually # check that code runs in parallel, but just that it produces # expected results. nthreads = 10 niter = 100 n = 20 a = csr_matrix(np.ones([n, n])) bres = [] class Worker(threading.Thread): def run(self): b = a.copy() for j in range(niter): _sparsetools.csr_plus_csr(n, n, a.indptr, a.indices, a.data, a.indptr, a.indices, a.data, b.indptr, b.indices, b.data) bres.append(b) threads = [Worker() for _ in range(nthreads)] for thread in threads: thread.start() for thread in threads: thread.join() for b in bres: assert_(np.all(b.toarray() == 2)) def test_regression_std_vector_dtypes(): # Regression test for gh-3780, checking the std::vector typemaps # in sparsetools.cxx are complete. for dtype in supported_dtypes: ad = np.matrix([[1, 2], [3, 4]]).astype(dtype) a = csr_matrix(ad, dtype=dtype) # getcol is one function using std::vector typemaps, and should not fail assert_equal(a.getcol(0).todense(), ad[:,0]) class TestInt32Overflow(object): """ Some of the sparsetools routines use dense 2D matrices whose total size is not bounded by the nnz of the sparse matrix. These routines used to suffer from int32 wraparounds; here, we try to check that the wraparounds don't occur any more. """ def __init__(self): # choose n large enough self.n = 50000 assert self.n**2 > np.iinfo(np.int32).max @dec.skipif(not sys.platform.startswith('linux'), "test requires Linux") @dec.skipif(np.dtype(np.intp).itemsize < 8, "test requires 64-bit system") def setUp(self): check_free_memory(5000) def tearDown(self): gc.collect() def test_coo_todense(self): # Check *_todense routines (cf. gh-2179) # # All of them in the end call coo_matrix.todense n = self.n i = np.array([0, n-1]) j = np.array([0, n-1]) data = np.array([1, 2], dtype=np.int8) m = coo_matrix((data, (i, j))) r = m.todense() assert_equal(r[0,0], 1) assert_equal(r[-1,-1], 2) del r gc.collect() @dec.slow def test_matvecs(self): # Check *_matvecs routines n = self.n i = np.array([0, n-1]) j = np.array([0, n-1]) data = np.array([1, 2], dtype=np.int8) m = coo_matrix((data, (i, j))) b = np.ones((n, n), dtype=np.int8) for sptype in (csr_matrix, csc_matrix, bsr_matrix): m2 = sptype(m) r = m2.dot(b) assert_equal(r[0,0], 1) assert_equal(r[-1,-1], 2) del r gc.collect() del b gc.collect() @dec.slow def test_dia_matvec(self): # Check: huge dia_matrix _matvec n = self.n data = np.ones((n, n), dtype=np.int8) offsets = np.arange(n) m = dia_matrix((data, offsets), shape=(n, n)) v = np.ones(m.shape[1], dtype=np.int8) r = m.dot(v) assert_equal(r[0], np.int8(n)) del data, offsets, m, v, r gc.collect() @dec.slow def test_bsr_1_block(self): # Check: huge bsr_matrix (1-block) # # The point here is that indices inside a block may overflow. def check(op): n = self.n data = np.ones((1, n, n), dtype=np.int8) indptr = np.array([0, 1], dtype=np.int32) indices = np.array([0], dtype=np.int32) m = bsr_matrix((data, indices, indptr), blocksize=(n, n), copy=False) del data, indptr, indices getattr(self, "_check_bsr_" + op)(m) del m gc.collect() for op in ("matmat", "matvecs", "matvec", "diagonal", "sort_indices", "transpose"): yield check, op @dec.slow def test_bsr_n_block(self): # Check: huge bsr_matrix (n-block) # # The point here is that while indices within a block don't # overflow, accumulators across many block may. def check(op): n = self.n data = np.ones((n, n, 1), dtype=np.int8) indptr = np.array([0, n], dtype=np.int32) indices = np.arange(n, dtype=np.int32) m = bsr_matrix((data, indices, indptr), blocksize=(n, 1), copy=False) del data, indptr, indices getattr(self, "_check_bsr_" + op)(m) del m gc.collect() for op in ("matmat", "matvecs", "matvec", "diagonal", "sort_indices", "transpose"): yield check, op @xslow def _check_bsr_matvecs(self, m): n = self.n # _matvecs r = m.dot(np.ones((n, 2), dtype=np.int8)) assert_equal(r[0,0], np.int8(n)) del r gc.collect() def _check_bsr_matvec(self, m): n = self.n # _matvec r = m.dot(np.ones((n,), dtype=np.int8)) assert_equal(r[0], np.int8(n)) del r gc.collect() def _check_bsr_diagonal(self, m): n = self.n # _diagonal r = m.diagonal() assert_equal(r, np.ones(n)) del r gc.collect() def _check_bsr_sort_indices(self, m): # _sort_indices m.sort_indices() @xslow def _check_bsr_transpose(self, m): # _transpose m.transpose() @xslow def _check_bsr_matmat(self, m): n = self.n # _bsr_matmat m2 = bsr_matrix(np.ones((n, 2), dtype=np.int8), blocksize=(m.blocksize[1], 2)) m.dot(m2) # shouldn't SIGSEGV # _bsr_matmat m2 = bsr_matrix(np.ones((2, n), dtype=np.int8), blocksize=(2, m.blocksize[0])) m2.dot(m) # shouldn't SIGSEGV @dec.skipif(True, "64-bit indices in sparse matrices not available") def test_csr_matmat_int64_overflow(): n = 3037000500 assert n**2 > np.iinfo(np.int64).max # the test would take crazy amounts of memory check_free_memory(n * (8*2 + 1) * 3 / 1e6) # int64 overflow data = np.ones((n,), dtype=np.int8) indptr = np.arange(n+1, dtype=np.int64) indices = np.zeros(n, dtype=np.int64) a = csr_matrix((data, indices, indptr)) b = a.T assert_raises(RuntimeError, a.dot, b) def test_upcast(): a0 = csr_matrix([[np.pi, np.pi*1j], [3, 4]], dtype=complex) b0 = np.array([256+1j, 2**32], dtype=complex) for a_dtype in supported_dtypes: for b_dtype in supported_dtypes: msg = "(%r, %r)" % (a_dtype, b_dtype) if np.issubdtype(a_dtype, np.complexfloating): a = a0.copy().astype(a_dtype) else: a = a0.real.copy().astype(a_dtype) if np.issubdtype(b_dtype, np.complexfloating): b = b0.copy().astype(b_dtype) else: b = b0.real.copy().astype(b_dtype) if not (a_dtype == np.bool_ and b_dtype == np.bool_): c = np.zeros((2,), dtype=np.bool_) assert_raises(ValueError, _sparsetools.csr_matvec, 2, 2, a.indptr, a.indices, a.data, b, c) if ((np.issubdtype(a_dtype, np.complexfloating) and not np.issubdtype(b_dtype, np.complexfloating)) or (not np.issubdtype(a_dtype, np.complexfloating) and np.issubdtype(b_dtype, np.complexfloating))): c = np.zeros((2,), dtype=np.float64) assert_raises(ValueError, _sparsetools.csr_matvec, 2, 2, a.indptr, a.indices, a.data, b, c) c = np.zeros((2,), dtype=np.result_type(a_dtype, b_dtype)) _sparsetools.csr_matvec(2, 2, a.indptr, a.indices, a.data, b, c) assert_allclose(c, np.dot(a.toarray(), b), err_msg=msg) def test_endianness(): d = np.ones((3,4)) offsets = [-1,0,1] a = dia_matrix((d.astype('f8'), offsets), (4, 4)) v = np.arange(4) assert_allclose(a.dot(v), [1, 3, 6, 5]) assert_allclose(b.dot(v), [1, 3, 6, 5]) def check_free_memory(free_mb): meminfo = get_mem_info_linux() if meminfo['memfree'] + meminfo['cached'] < free_mb * 1e6: raise SkipTest("test requires %d MB of free memory" % (int(free_mb),)) def get_mem_info_linux(): """ Get information about available memory. Returns a dict of items in /proc/meminfo """ info = {} with open('/proc/meminfo', 'r') as f: for line in f: p = line.split() info[p[0].strip(':').lower()] = float(p[1]) * 1e3 return info def get_own_memusage_linux(): """ Return the memory usage of the current process (in bytes) """ with open('/proc/%d/status' % os.getpid(), 'r') as f: procdata = f.read() m = re.search('VmRSS:\s*(\d+)\s*kB', procdata, re.S | re.I) if m is not None: memusage = float(m.group(1)) * 1e3 return memusage return np.nan if __name__ == "__main__": run_module_suite()